Proteases are widespread enzymes that control protein functions inside and outside a cell. Their well directed action is predominantly ensured by the availability of various more or less specific inhibitors, which themselves may be proteins. Cysteine proteases namely the thiol-dependent cathepsins are the most important intracellular proteolytic enzymes. The control of their activities is realized by limited proteolysis of their polypeptide chain, a change of the redox potential of their environment or by the inhibition via small peptide analogues as well as proteinaceous inhibitors. The by far most important protein inhibitors of cysteine proteases widely distributed are those of the chagasin and the cystatin family, respectively, well-known as relatively small (~10-12 kDa) and very robust monomeric proteins. Orthologous sequences are also found as oligo- and multi-domain single chain proteins consisting of up to eight cystatin domains that probably arise as a result of multiple events of gene duplications. Moreover, single and multiple cystatin domains that precede the prosequences of particular cathepsins, known as cathepsin F, can be identified in data bases. In these predicted and partially characterized proteins up to 17 cystatin domains are found, which in most cases are recognizable due to their typically conserved protease binding motifs. Although it may suggest itself that these domains are involved in the control of enzyme activities of endogenous and  exogenous proteases for the purpose of cell protection, the significance of multiple cystatin domains in these proteases is still completely unknown.